GBrowse-to-JBrowse Comparison

At first glance the JBrowse interface's leaner, cleaner look may strike users as too spare, as if much of the functionality has been lost. This is not the case. Rather, the menu/search/navigation area has been consolidated, leaving more space for the browser display. Although this "look and feel" is quite different, closer examination will reveal that much of the data and many of the navigational tools are shared between the browsers.

  1. Select Tracks
  2. The search box
  3. The drop-down list of assemblies
  4. The navigation buttons
  5. The chromosome-level view
  6. Positions in the detail view
  7. Track-specific menu for downloading and changing configuration
  8. Strain-specific variants
 

 

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GBrowse to JBrowse Detail Comparison

 

GBrowse

JBrowse

About JBrowse Functionality

1.  Selecting Tracks:



1.  Track selection is conveniently located as a list of available tracks in the left side bar.  The default is to show all the categories "collapsed" to give an overview and minimize scrolling. The number of tracks in that category is shown to the right of the category name. Enter a term, such as "disease" in the "filter" box at the top to reduce the available tracks to those matching your term. Click the red "X" to remove the term and restore all the tracks to availability.
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2.  The Search Box:

2.  The JBrowse search box is located between the lines for the chromosome-level position and the detail-level position (see #5 and 6 below) in the consolidated header region. Autocomplete, which offers suggestions based on what you have already typed, is included for object symbols.  For example, typing Ucp results in a list which includes the gene symbols Ucp1, Ucp2 and Ucp3, as well as the marker symbol "Ucp2_Ucp3"

Alternatively, enter the position as Chr#:start..stop. Selecting a different chromosome number in the dropdown to the left moves the selection to the same nucleotide position on a different chromosome.

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3.  Selection of Assemblies/Maps:

3.  The menu bar at the top of the window includes the dropdown to select a genome assembly. RGD currently has JBrowse instances for rat genome assemblies 3.4, 5.0 and 6.0; mouse build 37; and human builds 36.3 and 37.
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4.  Navigation

4.  The navigation buttons are located to the left of the search box.  As with GBrowse, the arrow buttons move the view about the distance of one screen left or right.  The larger zoom buttons zoom in or out about twice as far as the smaller buttons.

In addition to these buttons, JBrowse supports click and drag selection of regions in both the chromosome-level and detail-level position bars (see #5 and 6). 

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5.  The Chromosome-level Position Bar
6.  The Detail-level Position Bar

5 & 6.  The upper grey bar in the tool header gives the chromosomal position being shown in the detail display as a red vertical line or box. The lower gray bar at the bottom of the header region gives the chromosomal positions of the detail display below it. Light blue shading connects the ends of the outlined area in the chromosome view to the ends of the detail view below.
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7.  Context-specific Menus for Configuring Track Display and Downloading Track Data


7.  The context-specific menus for data tracks are still there, just hidden by default.  Click the down arrow on the title bar of the track to access menu options for changing the way the track is displayed and exporting data for that track ("Save track data").

"About this track" gives some additional information about a particular track such as the track type and category.

"Pin to top" causes that track to always be displayed directly beneath the header area at the top of the browser window.  By default tracks are displayed in the order they are turned on but they can be re-ordered by clicking and dragging the track title bar up or down.  When a line appears in the place you want the track to appear, release the mouse button and the track is dropped in that location.

"Edit Config" allows the user to directly edit the configuration script for a particular track.  This is not recommended for most users.

Individual tracks can be turned off in three ways:  by selecting "Delete track" in the context-specific menu, by clicking the X to the left of the track name, or by unchecking the box in the "Available Tracks" list in the side bar of the browser window.

"Save Track Data" opens a popup window with options for viewing and/or saving the data for a particular track.  Select to save either the data for the particular region you are viewing or, for some tracks, the entire dataset for that track.  The latter option is not available for large datasets such as the strain-specific variant tracks.  For this data, RGD has vcf files available on our ftp site.  In the "Save Track Data" popup select a file format, edit the name of the file, if desired, and choose whether to simply view the file online or save it to your local system.

Three "Display modes" are available:  "Normal" is the default view.  "Compact" reduces the height of each object in the track and turns off the display of object labels so that the height of the track is proportionally reduced even though each object can still be seen separately.  "Collapse" moves all objects to a single line on the track which in some cases results in overlap of individual objects.

Object labels are automatically displayed when the view is zoomed in sufficiently.  Uncheck the "Show labels" box to turn them off.

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8.  Strain-specific Variant Tracks

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8.  RGD's Strain-specific Variant tracks have been incorporated into the "Variants" category.  As additional strains are sequenced, and existing sequences are reanalyzed and remapped to additional assemblies, this data will be incorporated into JBrowse, not the deprecated GBrowse browser.

Strain-specific variant tracks are listed as the name of the substrain sequenced (e.g. ACI/Eur) and an abbreviation for the name of the lab or institution that did the sequencing and/or analysis.  For instance, "KNAW" stands for the Cuppen group at Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (Dutch: Koninklijke Nederlandse Akademie van Wetenschappen).